This is something I experienced while checking the new icon for notifications and I couldn't find a pattern. Sometimes it only works the first time, sometimes it works always, sometimes never.
Initially, I thought it was the gpii-app process exiting before the notification is created, but it's not the case. I added a setTimeout function to call "quit" and it didn't solve the issue. Apparently, is like Windows is not processing the notification but I'm not sure whether it's a problem coming from our win10 vagrant box or something going really wrong with electron/windows.